engleski

Proposal for an E-learning project - Visual database of highly repetitive DNA sequences

Non-coding DNA sequences represent ~98.5% of the human genome and are more than 50% repetitive. The function and evolution of the majority of them are not known. Leading scientists working in the field for decades still describe repetitive pericentromeric DNA sequences using terms such as: enigmatic, mysterious, conundrums, puzzles, black boxes, black holes, and the like. However, those functions of repetitive DNA that have been experimentally proven (in cell division, control of gene expression and aging), as well as the numerous functions that have been supposed (in speciation, generation of new genes, genome evolution, genome architecture, and programming) are highly important for both the life and the evolution of complex organisms. At the workshop I proposed a development of one common visual database of all available highly repetitive DNA sequences from diverse organisms. I proposed the mapping of reiterated DNA sequences to be based initially on the integration of two pioneering and mutually complementary computational models developed recently in Zagreb for the visualization of (peri)centromeric DNA organization. Both models, ColorHOR and SitRam, were positively evaluated in 2004 as original and valuable scientific contributions by reputed journals in bioinformatics (Bioinformatics and the Journal for Computational Biology and Chemistry, respectively). The models are the result of interdisciplinary work performed at the Rudjer Bošković Institute, the Department of Molecular Genetics ; the Pliva Research Institute ; the Faculty of Science, the Department of Physics ; the Rebro University Hospital, the Department of Internal Medicine ; the Croatian Academy of Sciences and Arts and at home. Since DotPlot, MapDraw and ColorHOR maps of highly repetitive DNA could be generated and interpreted in a very short time and in a very simple way, a database development is proposed to be realized in the frame of an E- learning project open to interested pupils and students. Besides the SitaRam and ColorHOR catalogs of repetitive DNA patterns, I propose that the database also includes a well-systematized archive of other visual material on highly repetitive DNAs produced either computationally or experimentally, together with related bibliography and available sequences of highly repetitive DNAs for performance of diverse bioinformatic experiments on them.

Database, pattern visualization, high-resolution DNA mapping, molecular evolution, (peri)centromeric DNA, (sub)telomeric DNA, satellite DNA, interspersed DNA, CENP-B boxes, higher-order organization, monomeric organization, gradient of divergence, unequal crossover

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